A collaborative expedition between Khaled bin Sultan Living Oceans Foundation, Cambridge Coastal Research Unit and Seychelles Centre for Marine Research and Technology – Marine Parks Authority (SCMRT-MPA) was conducted to the southern Seychelles, western Indian Ocean, in January 2005. This resulted in a series of habitat maps of the reefs and reef islands of the Amirantes Archipelago, derived from remotely-sensed Compact Airborne Spectrographic Imager (CASI) data. The procedures used in map development, image processing techniques and field survey methods are outlined. Habitat classification, and regional-scale comparisons of relative habitat composition are described. The study demonstrates the use of remote sensing data to construct digital habitat maps for the comparison of regional habitat coverage, a key function for coastal management.